3ZNJ

Crystal structure of unliganded ClcF from R.opacus 1CP in crystal form 1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure and Catalytic Mechanism of Chloromuconolactone Dehalogenase Clcf from Rhodococcus Opacus 1Cp.

Roth, C.Janosch, A.D.Kaschabek, S.R.Schloemann, M.Straeter, N.

(2013) Mol.Microbiol. 88: 254

  • DOI: 10.1111/mmi.12182
  • Primary Citation of Related Structures:  3ZNU, 3ZO7

  • PubMed Abstract: 
  • The actinobacterium Rhodococcus opacus 1CP possesses a so far unique variant of the modified 3-oxoadipate pathway for 3-chlorocatechol degradation. One important feature is the novel dehalogenase ClcF, which converts (4R,5S)-5-chloromuconolactone to ...

    The actinobacterium Rhodococcus opacus 1CP possesses a so far unique variant of the modified 3-oxoadipate pathway for 3-chlorocatechol degradation. One important feature is the novel dehalogenase ClcF, which converts (4R,5S)-5-chloromuconolactone to E-dienelactone. ClcF is related to muconolactone isomerase (MLI, EC 5.3.3.4). The enzyme has a ferredoxin-type fold and forms a homodecamer of 52-symmetry, typical for the MLI family. The active site is formed by residues from two monomers. The complex structure of an E27A variant with bound substrate in conjunction with mutational studies indicate that E27 acts as the proton acceptor in a univalent single-base syn-dehydrohalogenation mechanism. Despite the evolutionary specialization of ClcF, the conserved active-site structures suggest that the proposed mechanism is representative for the MLI family. Furthermore, ClcF represents a novel type of dehalogenase based on an isomerase scaffold.


    Related Citations: 
    • Crystallization and Preliminary Characterization of Chloromuconolactone Dehalogenase from Rhodococcus Opacus 1Cp.
      Roth, C.,Kaschabek, S.R.,Groning, J.A.D.,Handrek, T.,Schlomann, M.,Strater, N.
      (2012) Acta Crystallogr.,Sect.F 68: 591


    Organizational Affiliation

    Center for Biotechnology and Biomedicine, Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5-CHLOROMUCONOLACTONE DEHALOGENASE
1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, R, S, T, U, V, W, X, Y, Z, a, b, c, d, e, f
94Rhodococcus opacusGene Names: clcF
EC: 5.3.3.4
Find proteins for Q8G9L0 (Rhodococcus opacus)
Go to UniProtKB:  Q8G9L0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, 9, A, a, b, B, C, c, d, D, E, e, f, F, G, H, I, J, K, L, M, N, O, P, R, S, T, U, V, W, X, Y, Z
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, 9, a, A, b, B, C, c, D, d, E, e, f, F, G, H, I, J, K, L, M, N, O, P, R, S, T, U, V, W, X, Y, Z
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 151.140α = 90.00
b = 79.430β = 93.41
c = 198.970γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-03-20
    Type: Atomic model, Other
  • Version 1.2: 2013-04-24
    Type: Database references